GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Acidovorax sp. GW101-3H11

Best path

ans, aatJ, aatQ, aatM, aatP

Also see fitness data for the top candidates

Rules

Overview: Asparagine catabolism in GapMind is based on asparaginase, which forms ammonia and aspartate. The asparaginase may be secreted or cytoplasmic. Asparatate can be transaminated to oxaloacetate, which is an intermediate in central metabolism.

34 steps (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase Ac3H11_1866 Ac3H11_2391
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ Ac3H11_1642 Ac3H11_1955
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) Ac3H11_1956 Ac3H11_3326
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) Ac3H11_1957 Ac3H11_3200
aatP aspartate/asparagine ABC transporter, ATPase component Ac3H11_1958 Ac3H11_3327
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Ac3H11_3326
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Ac3H11_1958 Ac3H11_3327
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Ac3H11_3326 Ac3H11_2554
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP
bgtA aspartate ABC transporter, ATPase component BgtA Ac3H11_3327 Ac3H11_3200
bgtB' aspartate ABC transporter, permease component 1 (BgtB) Ac3H11_3326
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) Ac3H11_1956
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) Ac3H11_3326
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) Ac3H11_1958 Ac3H11_3327
dauA dicarboxylic acid transporter DauA Ac3H11_3820
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ Ac3H11_1958 Ac3H11_4899
glt aspartate:proton symporter Glt Ac3H11_719 Ac3H11_1083
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) Ac3H11_3326 Ac3H11_2554
natH aspartate ABC transporter, permease component 2 (NatH) Ac3H11_2554 Ac3H11_1957
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) Ac3H11_2554 Ac3H11_1957
peb1C aspartate ABC transporter, ATPase component Peb1C Ac3H11_3200 Ac3H11_3327
peb1D aspartate ABC transporter, permease component 2 (Peb1D) Ac3H11_2554
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory